Owing to their high throughput screening capability, microarrays have become an essential tool for the healthcare and pharmaceutical industries where researchers are working to diagnose disease or discover new drugs. Moreover, agriculture and homeland defense firms are utilizing microarrays to uncover information regarding the presence of harmful pathogenic bacteria. Such simultaneous screening is possible by printing many microscopic spots, typically 10-250 μm in size, of biological molecules (i.e., biomolecules such as nucleic acid fragments, antibodies, peptides, proteins, pathogens, cells and the like) as probes onto the same substrate to form a microarray. A high density microarray developed for research purposes typically comprises between 1000 to 50000 probe spots arranged in a predetermined regular pattern on a substrate, thus leading to a spot density of about 50 spots/cm2 to 2500 spots/cm2. The dimension of the substrate can vary, but generally the substrate is the size of a 1 inch by 3 inch microscope slide. It is critical that the substrate surface be reactive and capable of binding probe biomolecules of known sequence. In use, the microarray is hybridized with target bio-molecules of unknown sequence in order to simultaneously detect the response of the target with the different probes spotted on the array surface. Typically, targets are labeled with fluorescent dyes and fluorescence based detection techniques are most commonly used to quantify the response of the target biomolecule to the probes following hybridization. The composite quantitative response of the target to all the probes spotted on the microarray substrate is the data resulting from the microarray experiment.
Microarray experiments can be employed to detect the expression levels of various genes or proteins for a given organism (i.e. human, mouse, plant, bacteria, etc). Highly expressed genes or proteins are much easier to detect because their concentration in a given sample is often the greatest. However, when expression levels are low or samples are scarce, sensitive and reliable detection technology becomes critical. This type of detection technology is increasingly important for studying protein-protein interactions or protein biochemical activity since the concentration of proteins can not be amplified via enzymatic reactions such as the polymerase chain reaction.
As a result, within the microarray industry, there is an overriding need for confident detection of low abundant protein and/or nucleic acids. When attempting to accurately measure or detect such low levels in a microarray experiment, it is imperative that researchers employ system components that maximize sensitivity and overall signal to noise ratio. A number of approaches can be employed to impact sensitivity and signal to noise ratio and three of the common ones are as follows: (1) improvements in the sensitivity or detection limits of scanning devices, (2) increased amplification of the fluorescent signal via labeling methods, and (3) the employment of a highly sensitive substrate. The present invention focuses on enhancing signal to noise ratio through the employment of a highly sensitive microarray substrate.
An increase in signal strength can be achieved by increasing the number of binding sites per unit area (functional site density), which ultimately impacts the retention of immobilized bio-molecular probes and the emission of an increased signal when hybridized with fluorescently labeled target molecules. Signal clarity can also be enhanced through a reduction in the inherent auto-fluorescence of the materials and/or system used for detection. These approaches will ultimately influence the signal to noise ratio, either by increasing the signal strength, and/or reducing the noise. Several prior art approaches have been attempted.
Many common methods used to manufacture high density microarrays use non-porous, two-dimensional glass substrates containing functional sites for binding samples of interest. Glass is preferred because of its inertness and low inherent auto-fluorescence which contributes less noise to the signal being detected, usually measured by fluorescence-based techniques. Examples of such commercially available substrates are UltraGAPS II® slides (Corning Inc., Life Sciences, Oneonta, N.Y.), Nexterion® Slides (Schott North America, Inc., Louisville, Ky.), and Array-It® slides (Telechem International Inc., Sunnyvale, Calif.). One drawback to using non-porous glass is that the functional site density is quite low resulting in relatively weak signals, which makes it very difficult to detect the sample of interest, especially when trying to detect low expressing genes or proteins. This effect can be minimized by increasing the volume or concentration of the sample of interest, however, the approach can only be employed if a large enough sample is available. Often, researchers are highly limited by the quantity, concentration or volume of a given sample. A common approach to increasing functional site density has been through the use of porous substrates to increase the accessible surface area containing the functional sites. Tanner et al. (U.S. Pat. No. 6,750,023) teach a method of forming a functional material for attaching an array of biological or chemical analytes by applying an inorganic porous layer to an inorganic non-porous understructure.
Alternate approaches using organic polymers as functional materials have been attempted. Haddad et al. (WO 01/66244) teach making arrays utilizing textured non-porous functional materials created from oriented polymer films. Porous organic polymers have also been used in microarray substrates and examples of such commercially available materials are Vivid Microarray® Slides (Pall Corporation, East Hills, N.Y.) and CAST® slides (Schleicher & Schuell Biosciences, Inc., Keene, N.H.), both using porous nylon membranes.
Phase inversion is a common technique used to make microporous membranes from organic polymers. Use of such membranes as microarray substrates is described in detail in U.S. Patent Applications 2003/0219816 of Solomon et al and 2004/0157320 of Andreoli et al. A variety of microporous materials are discussed in the literature, with nylon and nitrocellulose being the most common. Nylon affords the benefits that it can be readily rendered microporous and has a natural affinity for DNA. Similarly, nitrocellulose is known to be effective in binding proteins. In the case of nylon and nitrocellulose, binding with DNA and/or proteins is reliant on the inherent functional groups present in the nylon or nitrocellulose polymer backbone. Consequently, the functional site density afforded by these materials is limited. Moreover, the pore size of phase inversion membranes may not be small enough to prevent lateral spot spreading which leads to crosstalk thereby limiting the array density. Another common problem with using organic polymers such as nylon or nitrocellulose resides with the fact that these materials possess inherently high auto-fluorescence. Since fluorescence-based detection is the most commonly used technique to quantify the hybridized target biomolecules, high auto-fluorescence contributes to increased background noise thereby adversely affecting the clarity of the fluorescent signal. Use of pigments such as carbon black has been shown to reduce the auto-fluorescence. Alternatively, as taught by Montagu (WO 2004/018623), the background noise can also be reduced by the use of a thin (less than about 5μ) functional material.
The need exists for an array substrate that can be easily fabricated, provides high functional site density and exhibits low auto-fluorescence to maximize signal to noise ratio. The present invention addresses all of these needs along with providing very high level of precision.